Human liver cancer, with increasing occurrence in the United States, is the 5th most prevalent malignant disease in the world. It is the fourth leading cause of cancer mortality, which accounts for an estimated 1 million deaths annually. Hepatocellular carcinoma (HCC) is a major type of primary liver cancer. HCC is considered to be a terminally ill disease and currently, there is little progress toward the discovery of efficient therapies leading to regression. This is due largely to the lack of a method for early diagnosis and the lack of information on the phenotypic changes associated with the development of HCC. Our goals are to identify common gene clusters that are responsible for the genesis of HCC and to discover new genes critical for viral hepatitis-mediated HCC as well as genes necessary for metastasis. These studies will contribute to the establishment of novel markers with potential diagnostic and prognostic value, and analysis of these genes would provide further understanding of the genesis of liver cancer and provide further insights into designing strategies for HCC-directed molecular therapy. We have taken two approaches, namely, Serial Analysis of Gene Expression (SAGE) and cDNA microarray, to explore potential cellular genes that are expressed abnormally in primary human hepatocytes infected with the two viral hepatitis oncoproteins, HBx or HC-core, and in liver samples from chronic active hepatitis patients or HCC patients that differ in the status of HBV or HCV. In addition, we are comparing gene expression profiles between primary HCC and metastatic HCC. Infection of normal hepatocytes with HBx and HC-core is achieved by a replication-defective adenoviral vector. Using SAGE, we have constructed a library derived from primary human hepatocytes infected with HBx. Analysis of over 19,000 transcripts (representing 1443 unique genes) provides a distribution of transcriptomes characteristic of normal hepatocytes. In the HBx-expressing hepatocytes, a total of 57 transcripts were induced and 46 transcripts were repressed with greater than 5-fold. Interestingly, most of transcripts that are upregulated by HBx expression are clustering in three major classes including genes that encode ribosomal proteins, transcription factors with zinc finger motifs and proteins associated with protein degradation pathway. These results suggest that HBx may function as a major regulator in a common cellular pathway that in turns regulating protein synthesis, gene transcription and protein degradation. In addition, we have compared gene expression profiles in primary hepatocytes expressing HBx as well as liver samples from chronic liver diseases including HBV or HCV infection and in HCC. Clustering algorithms were used to identify deregulation of distinctive gene expression profiles in these samples. Northern blotting analysis was used to verify the microarray data. We have identified multiple genes that are either up- or down-regulated in these samples. Further analysis of these genes will be useful for understanding the mechanism of HBV- and HCV-mediated oncogenesis.